Tao Kaifeng, Tang Lu, Luo Yan, Li Lu
College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China.
Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan, 650224, China.
BMC Plant Biol. 2025 Jan 10;25(1):37. doi: 10.1186/s12870-024-06040-1.
Phaius Lour. (Collabieae, Orchidaceae) is a small genus consisting of about 45 species, with highly ornamental and medicinal values. However, the phylogenetic relationship of Phaius among Calanthe s. l. has been highly debated based on morphological and molecular data. The complete chloroplast (cp) genome has been widely used as a useful molecular marker for resolving phylogenetic problems, while few genomic data on Phaius was available. Therefore, complete cp genomes of eight Phaius species were sequenced and characterized in detail to provide a better understanding of its phylogenetics in Calanthe s. l.
The cp genomes of eight species investigated exhibited conserved quadripartite structures with varied lengths ranging between 157,997 bp to 158,735 bp. The overall GC content of these genomes ranged between 36.82 and 36.97%. Gene annotation revealed 136 genes in all eight genomes, of which 21 were duplicated in inverted regions and 15 with introns. Comparative analysis of eight cp genomes revealed stable sequence identity with greater variation in the single-copy regions, alongside notable differences in the genes at the LSC/IRb and IRb/SSC junctions, as well as in the number of SSRs. The phylogenetic analysis based on CDS from 49 complete cp genomes of Collabieae indicated that the eight Phaius species, together with other two species P. philippinensis and P. hainanensis, were clustered into a monophyletic clade among Calanthe s. l. and divided into two subclades with strong supports. Additionally, it was also supported that Calanthe s. l. should be divided into five genera with strong supports, including Calanthe s. s., Cephalantheropsis, Styloglossum, Phaius, and Preptanthe.
It was the first report on the complete cp genome of six Phaius species (P. columnaris, P. mishmensis, P. takeoi, P. tonkinensis, P. wallichii and P. wenshanensis) and has been comparatively analyzed in detail with P. flavus and P. tancarvilleae. It provided a comprehensive investigation of various cp genomic features for phylogenetic implications, including overall genome structure, codon usage, repeat sequences, IR boundaries, DNA polymorphisms, and phylogenetic reconstruction. It was suggested that Phaius and Calanthe s. s. should be treated as two independent genera. The concept of new genus Paraphaius was not confirmed by complete cp genomic data here. The intergeneric relationship of Phaius and its alliance in Calanthe group could be understood better by more cp genomic data.
鹤顶兰属（Collabieae，兰科）是一个小属，约有45个物种，具有很高的观赏和药用价值。然而，基于形态学和分子数据，鹤顶兰属在广义虾脊兰属中的系统发育关系一直存在激烈争论。完整的叶绿体（cp）基因组已被广泛用作解决系统发育问题的有用分子标记，而关于鹤顶兰属的基因组数据却很少。因此，对8种鹤顶兰属植物的完整cp基因组进行了测序和详细表征，以便更好地了解其在广义虾脊兰属中的系统发育。
所研究的8个物种的cp基因组呈现出保守的四分体结构，长度在157,997 bp至158,735 bp之间变化。这些基因组的总体GC含量在36.82%至36.97%之间。基因注释显示，所有8个基因组中共有136个基因，其中21个在反向区域重复，15个含有内含子。对8个cp基因组的比较分析显示，单拷贝区域的序列一致性稳定，但变异较大，同时在LSC/IRb和IRb/SSC边界处的基因以及简单序列重复（SSR）的数量上存在显著差异。基于Collabieae科49个完整cp基因组的编码序列进行的系统发育分析表明，这8种鹤顶兰属植物与另外两种菲律宾鹤顶兰和海南鹤顶兰一起，在广义虾脊兰属中聚为一个单系分支，并分为两个得到有力支持的亚分支。此外，也有力支持广义虾脊兰属应分为5个属，包括狭义虾脊兰属、头蕊兰属、舌唇兰属、鹤顶兰属和Preptanthe属。
这是关于6种鹤顶兰属植物（柱叶鹤顶兰、米什米鹤顶兰、武氏鹤顶兰、东京鹤顶兰、大花鹤顶兰和文山鹤顶兰）完整cp基因组的首次报道，并与黄花鹤顶兰和坛花鹤顶兰进行了详细的比较分析。它对各种cp基因组特征进行了全面研究，以探讨其系统发育意义，包括整体基因组结构、密码子使用、重复序列、IR边界、DNA多态性和系统发育重建。建议将鹤顶兰属和狭义虾脊兰属视为两个独立的属。这里的完整cp基因组数据未证实新属拟鹤顶兰属的概念。通过更多的cp基因组数据可以更好地理解鹤顶兰属及其在虾脊兰类群中的近缘属间关系。
